[Debian-med-packaging] Bug#831188: libgenome: FTBFS with GCC 6: gnDefs.cpp:8:20: error: 'int64 abs(int64)' conflicts with a previous declaration

[Lucas Nussbaum]

Source: libgenome
Version: 1.3.1-8
Severity: serious
Tags: stretch sid
User: debian-qa at lists.debian.org
Usertags: qa-ftbfs-20160713 qa-ftbfs
Justification: FTBFS with GCC 6 on amd64

Hi,

During a rebuild of all packages in sid using the gcc-defaults package
available in experimental to make GCC default to version 6, your package failed
to build on amd64. For more information about GCC 6 and Stretch, see:
- https://wiki.debian.org/GCC6
- https://lists.debian.org/debian-devel-announce/2016/06/msg00007.html

Relevant part (hopefully):
> /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gnDefs.lo gnDefs.cpp
> libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c gnDefs.cpp  -fPIC -DPIC -o .libs/gnDefs.o
> gnDefs.cpp: In function 'int64 abs(int64)':
> gnDefs.cpp:8:20: error: 'int64 abs(int64)' conflicts with a previous declaration
>  int64 abs( int64 a ){
>                     ^
> In file included from /usr/include/c++/6/stdlib.h:36:0,
>                  from ../libGenome/gnSetup.h:19,
>                  from ../libGenome/gnDefs.h:24,
>                  from gnDefs.cpp:5:
> /usr/include/c++/6/cstdlib:180:3: note: previous declaration 'long long int std::abs(long long int)'
>    abs(long long __x) { return __builtin_llabs (__x); }
>    ^~~
> make[3]: *** [gnDefs.lo] Error 1

The full build log is available from:
   http://people.debian.org/~lucas/logs/2016/07/13/libgenome_1.3.1-8_unstable_gcc6.log

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.